Variant report

Variant	rs12871645
Chromosome Location	chr13:50931565-50931566
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:50697643..50701953-chr13:50927459..50931609,5	MCF-7	breast:
2	chr13:50921012..50924496-chr13:50928221..50931667,4	MCF-7	breast:
3	chr13:50931295..50934143-chr13:50939870..50941977,3	MCF-7	breast:
4	chr13:50931287..50933893-chr13:50934421..50935929,2	MCF-7	breast:
5	chr13:50929110..50931942-chr13:50932169..50935113,3	MCF-7	breast:
6	chr13:50929441..50932225-chr13:50939480..50941358,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DLEU7-10	chr13:50931233-50931777	NONHSAT033837

No data

Variant related genes	Relation type
ENSG00000231607	Chromatin interaction
ENSG00000223676	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11842790	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12853498	1.00[CEU][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12855386	1.00[ASN][1000 genomes]
rs12867018	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12874278	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12874827	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12876227	1.00[ASN][1000 genomes]
rs17074093	1.00[CEU][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17074141	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17074143	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17074145	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17363026	1.00[ASN][1000 genomes]
rs17363566	1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066664	1.00[ASN][1000 genomes]
rs2066673	1.00[ASN][1000 genomes]
rs2066679	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3095158	0.87[ASN][1000 genomes]
rs3095160	0.87[ASN][1000 genomes]
rs3095164	0.87[ASN][1000 genomes]
rs3095165	0.87[ASN][1000 genomes]
rs3116594	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3116595	0.87[ASN][1000 genomes]
rs3118648	0.87[ASN][1000 genomes]
rs3118649	0.87[ASN][1000 genomes]
rs3118650	0.87[ASN][1000 genomes]
rs34042295	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34357487	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34374535	1.00[ASN][1000 genomes]
rs34453016	1.00[ASN][1000 genomes]
rs34556868	1.00[ASN][1000 genomes]
rs34700115	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34712361	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34972893	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35299189	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35383320	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35413012	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35542898	1.00[ASN][1000 genomes]
rs35650342	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35902227	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35980102	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67217502	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67964536	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs706603	1.00[ASN][1000 genomes]
rs71428294	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71436217	1.00[ASN][1000 genomes]
rs71436218	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71436219	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71436220	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71436222	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7986582	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7990202	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs806315	1.00[ASN][1000 genomes]
rs806318	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9596268	0.87[CEU][hapmap]
rs9596270	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2752608	chr13:50550099-51054499	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1249 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12871645	AGPAT4	trans	brain	seeQTL

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50926600-50933000	Enhancers	Liver	Liver
2	chr13:50926600-50934800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr13:50928400-50931600	Weak transcription	Aorta	Aorta
4	chr13:50928400-50932400	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr13:50928600-50932400	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr13:50928800-50931600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr13:50929000-50931600	Weak transcription	HSMMtube	muscle
8	chr13:50929200-50934200	Weak transcription	Lung	lung
9	chr13:50929200-50934400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr13:50929400-50932400	Weak transcription	Thymus	Thymus
11	chr13:50929600-50932400	Weak transcription	Dnd41	blood
12	chr13:50929600-50932600	Weak transcription	Primary B cells from cord blood	blood
13	chr13:50929800-50933800	Weak transcription	Primary T cells from cord blood	blood
14	chr13:50930000-50932800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr13:50930000-50935800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr13:50930200-50932400	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr13:50930200-50933600	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr13:50930200-50939200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr13:50930200-50939600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr13:50930400-50932200	Weak transcription	Primary B cells from peripheral blood	blood
21	chr13:50930400-50932400	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr13:50930400-50932600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr13:50930400-50932600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr13:50930600-50932400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr13:50930800-50931800	Enhancers	Pancreas	Pancrea
26	chr13:50930800-50933800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr13:50930800-50934000	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr13:50930800-50935000	Enhancers	Fetal Thymus	thymus
29	chr13:50931000-50932800	Enhancers	Placenta Amnion	Placenta Amnion
30	chr13:50931000-50932800	Enhancers	NHDF-Ad	bronchial
31	chr13:50931000-50933000	Enhancers	Fetal Muscle Leg	muscle
32	chr13:50931000-50933200	Enhancers	Fetal Heart	heart
33	chr13:50931000-50933400	Enhancers	Fetal Lung	lung
34	chr13:50931200-50931600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr13:50931200-50931800	Enhancers	Brain Anterior Caudate	brain
36	chr13:50931200-50931800	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr13:50931200-50932200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr13:50931200-50932400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr13:50931200-50932800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr13:50931200-50932800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr13:50931200-50932800	Enhancers	Fetal Kidney	kidney
42	chr13:50931200-50932800	Enhancers	Fetal Stomach	stomach
43	chr13:50931200-50932800	Enhancers	Gastric	stomach
44	chr13:50931200-50932800	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr13:50931200-50932800	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr13:50931200-50932800	Enhancers	K562	blood
47	chr13:50931200-50932800	Enhancers	NHLF	lung
48	chr13:50931200-50932800	Enhancers	Osteobl	bone
49	chr13:50931200-50933000	Enhancers	Pancreatic Islets	Pancreatic Islet
50	chr13:50931200-50933000	Enhancers	NH-A	brain

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